I tried it at practice this weekend and sorta unconsciously put in my FX loop. And it made this horrible low end biting noise and I thought my amp was going to blow up !?

I've since learned that the placement in front is best, like the customary placement of a regular Wah pedal. I've always had simple delay/reverb/flanger/comps, nothing so thrilling as this new pedal...

Anyway do we know why it would make such an awful noise in the loop? I mean everytime I hit my strings, even with the threshold on the pedal realtively low it was like =wap= =pop= awful. Could it be that it was accentuating all my amp EQ settings, including the low end?

Not knowing anything about what amp you used or what type of effects loop it has, I can only make a guess. The most likely cause of the bad sound is that the loop was sending a line-level signal to a floor pedal effect that wants to see an instrument-level signal, causing the effect's circuit to overload, creating some nasty, unmusical sounding distortion. If your loop has an adjustable send level knob or a switch to change its operating level (line/instrument) you might try experimenting with those. Usually, the simpler effects loops (without those features) are designed specifically to work only with rack type gear running at higher line signal levels and not with stomp box type effects.

Some pedals should NOT be run in loops at all - overdrives, distortions and fuzzes in particular, but any other which have high gain can be a problem (eg compressors set very extremely)... I think I've come across it with a wah-type effect before too, where the 'tuned' nature of the sound somehow interacted with the amp.

It's because the amp can become unstable, due to 'coupling' between the circuitry after the loop and that before, via the power supply usually. This sets up a closed feedback loop, and if there's enough gain in the system introduced by the effect pedal, it will self-oscillate - possibly outside the range of your hearing, you may just hear a bad distorted tone or a severe loss of volume and very odd tonality. In really extreme (and rare) cases it can actually damage the amp.

Don't do it... it usually doesn't sound good anyway, even if the amp is fine. The only types of effects which should really be in the loop are modulation and delay-based ones, and EQ and mild boosts, or possibly a compressor used more as a soft limiter, where it isn't bringing the no-signal gain up a long way.

Below is an excerpt from the Egnater MOD100 manual. It has some useful information about loops in general:
MOD100
Effects Loop Operation

The Egnater effects interface is the most versatile loop system you will find anywhere. There are two totally independent, tube buffered loops, each optimized for specific applications.

1) Series Loop:
Basically an insert patch point. When an external effect is patched into the series send and return jacks, the path is interrupted and 100% of the signal is routed through the effect. This puts some special demands on the effects unit. It must be essentially transparent, meaning it shouldnt mess with your tone. The input and output levels must be properly set for maximum headroom and lowest noise and it needs to operate at line level. Proper setting of the levels can be achieved using the following method.
a) Set your amp/preamp volume levels for normal playing levels. Connect a high quality shielded cable from the series send jack to the effect input.
b) Adjust the effects unit input level to just peak while playing your most aggressive licks.
c) Now connect another high quality shielded cable from the effect output to the return jack.
d) Adjust the effects unit output level to the match the volume you heard before connecting the return cable. You can check this by pulling the cable in and out of the return jack while playing and verifying there is no substantial volume difference. This is called unity gain. A cool techie phrase for you get out what you put in.
2) Parallel Loop:
This is a more specialized loop. It has the advantage of maintaining your dry signal (it doesnt mess with your tone), while allowing you to mix in the amount of effect you want. The MOD100 parallel loop is a bit different than most. Typically, parallel loops found on guitar amplifiers have a wet/dry mix control that turns down the dry signal (messing with your tone) while simultaneously turning up the effects level. The MOD100 parallel loop is unique in that it never messes with your dry tone. It simply mixes in the amount of effects using the effect knob on the front panel, much like the effects buss on a mixing console. The direct signal remains unaltered and the effects are simply mixed back in. There are a few basic rules that must be adhered to. This also puts some limitations on the uses for the parallel loop.
a) Your effects unit must be set for 100% wet. This means to set the mix levels on the effect so that there is no dry signal passing through the unit. Think of the mixing console again. You would not want to have any dry signal going through the effects buss because you would then be mixing in not only the effect but also the unwanted dry signal that comes out of the effects unit. This can even be detrimental to your tone because the dry output signal of many effects units is out of phase with the input. Consequently, as you turn up the effects return knob, you may actually be mixing the icky out of phase signal back in with your awesome dry signal and you guessed it .messing with your tone. Often loops on guitar amps are said to suck tone. This tone sucking is more likely caused by improperly setting the effects mix than the loop design.

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Effects loops continued:

3) Now lets address the specific uses, advantages, disadvantages and limitations of each loop.
a) The series loop, by nature of the fact that it breaks the direct path and processes 100% of the signal, makes it so that essentially any line level gadget will work. You can use echo, reverb, noise reduction, tremolo, equalizers etc in this loop. Remember to follow the procedure for setting for unity gain.
Advantages are:
Works fine with just about any effect.
No special requirements, other than the unity gain settings, are needed.
Basically Plug and Play.
Disadvantage is that your entire signal passes through the effects unit and may mess with your tone.

b) The parallel loop, on the other hand, has more limited uses but has the distinct advantage of not messing with your tone. This loop is ideally suited for what are called time based effects. This includes echo, reverb, chorus, flanging. These types of effects work in parallel with your direct signal (think about the mixer again). Now the bad news remember the dry signal is always present. You cannot use effects that require processing 100% such as equalizers, noise reduction/gates, tremolo or compressor/limiters.
Advantages are:
Doesnt mess with your tone.
Easy to adjust the effects level with the front panel knob.
Disadvantage is the limited uses and may require reprogramming your effects unit.

4) Special Notes:
a) A concern is the fact that many multi-effects units have a combination of all of the different effects. This means, using the parallel loop, you must be aware of which effects can and cant be used. For ease of operation, we recommend using the series loop if you intend to use a mix of different time based and non-time based effects in one unit.
b) Both loops are for line level operation. Though some floor type and tabletop effects may work, the loops are designed basically for rack mount type effects units. Not guitar level floor pedals. You will know an effect is not made for line level if, when you plug it into the loop, you notice distortion and a loss of volume.

I went home and tried out a new way, no FX loop , with an additional twist, with the goal of simplifying my rig even more.....:Removing my channel switcher !(yet another cord going to the back of the amp)

and using my fave channel 1 (Marshall-type) for everything !

Even cleans. How I do this? - by bringing way down the level knob on my Compressor pedal so that when the compressor is on for cleans (which is the only time I use the comp), the signal is far less hot and therefore less hit on the preamp tubes...not chimy Fendery like it was before but hey our other guitar player does that. So basically my compressor is acting as a clean/dirty channel switcher like I was used to before.

the reverb and the delay behaved fine with the clean tones, maybe a little darker. Then, mushy chaotic and totally cool to me when using them with a dirty tone - which is extreemly rare, maybe for a few solos I have the delay on for it. But it was liquidy and out of control and it sounded so cool ! Like an old concert bootleg from the 70's or something.

my EQ pedal is now really helping, I have a cut at 400 hz and a boost at 800 and thats it. Totally cleans the dirty tone up and I get barky authoritative spank out of it. Clears up the clean tones too. I know my SD Custom Custom pickup is part of the mud, but I wouldn't trade that thing for any other pickup.

that Guyatone WR-3 Wah Rocker pedal is a little irritating though- its got some added low end going on. So I put the threshold at its least sensitive and stick to the higher strings (which I used it for anyway). This way my fret hand sloppily hitting the lower strings won't set it off as easily.

this was at bedroom volume..... band volume I can tell the new way will work, just need to cut down the bass on the amp a little. We'll see!